[BioC] Adding annotations to fit2

[john seers (IFR)]

Hi Sally

Is fit2 by any chance the output from limma fitting a linear model? If
not this is not relevant.

If it is so I think you may be able to do something like 

	fit2$genes<-cbind(fit2$genes, MGLnew)

If that does not work, if you are using topTable a bit later, you can do
something like this: 
       
       tt<-topTable(eb, number=ngenes, genelist=cbind(eb$genes, MGLnew))
       
       
       	Regards
       	John

 
---

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Sally
Sent: 17 February 2009 03:35
To: bioconductor at stat.math.ethz.ch
Cc: Sally
Subject: [BioC] Adding annotations to fit2

I want merge fit2 with a txt file I'll call MGL (mastergenelist) which
contains gene id information.  I am using a custom cDNA array.  The
reason is that I want the gene ID information along-side the rownames
(which are the accession IDs).  Both have identical row names.  MGL has
missing data.

I have tried:

MGLnew<-read.table(file="MGL.txt",sep="\t",header=TRUE,na.strings="",fil
l=TRUE)  #WORKS
write.table(MGLnew,file="MGLnew.txt",sep="\t") #WORKS
fit2<-merge(fit2,MGLnew,by="row.names")  #NOT WORKING

When I run this I get the following error message:

Error in dim(data) <- dim : attempt to set an attribute on NULL

What does this error message mean?  How do I fix the problem?

Sally Goldes

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